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1yeb

STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN

Method: X-RAY DIFFRACTION Dmax: 47.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C

Saccharomyces cerevisiae

UniProt P00045

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 6–111 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.95 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1YEB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YEA STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN Deposited 1991-10-29 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–113（112 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1YTC THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS Deposited 1995-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–113（112 aa）
Mutation：N52I Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
3CXH Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer. Deposited 2008-04-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 23-meric
Chain W 2–113（112 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UMQ UNDECYL-MALTOSIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 SMA STIGMATELLIN A × 2 8PE (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate × 2 CN6 (2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate × 2 9PE (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate × 2 7PH (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 6PH (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch (Paraffin oil)；pH 7.5；277 K；1M Sucrose, 10% DMSO, 20mM Tris pH 7.5, 80mM NaCl, 0.05 % UM, 1 M stigmatellin, 5% PEG 4000, Microbatch (Paraffin oil), temperature 277K
Resolution 2.50 Å R-free 0.256

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC7_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–106； UniProt 6–111

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1yeb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yeb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yeb
Deposition date deposition_date1991-10-29
Structure title titleSTRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN
Keywords keywordsELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.23 Å
Radius of gyration Rg (electron density) rg_electron12.83 Å
Forward intensity I(0) i03403970.00
Molecular weight molecular_weight12824.0 kDa
Excluded volume excluded_volume15985 ų
Envelope volume envelope_volume17180 ų
Hydration-shell volume shell_volume11275 ų
Envelope diameter envelope_diameter44.6 Å
Shell Rg shell_rg18.81 Å
Envelope Rg envelope_rg13.24 Å
Shape Rg shape_rg12.79 Å
Total Rg total_rg14.24 Å
Total atoms total_atoms898
Residues n_residues107
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax47.1 Å
Rg (real space) rg_real14.11 Å
Rg uncertainty (real space) rg_real_error0.22 Å
I(0) (real space) i0_real3.4040e+06
I(0) uncertainty (real space) i0_real_error3.8370e+04
Rg (reciprocal space) rg_reciprocal14.12 Å
I(0) (reciprocal space) i0_reciprocal3404000.0000
Solution quality estimate total_estimate0.7926
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.1 Å
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.287
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha628500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1yeba_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c

CATH v4.4 (1 domains)

Domain ID domain_id1yebA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
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8. Citations (1)

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9. Files and Curves (10)